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‘ordr’ package

A unified framework for ordination objects and biplot methods using tidy principles

ordr ordr-package
ordr package

Functions, classes, and methods

Introducing and adapting ordination techniques for the ordr workflow

lda_ord() predict(<lda_ord>) model.frame(<lda_ord>)
Augmented implementation of linear discriminant analysis
lra() print(<lra>) screeplot(<lra>) biplot(<lra>) plot(<lra>)
Log-ratio analysis
eigen_ord() svd_ord() cmdscale_ord() cancor_ord()
Wrappers for lossy ordination methods

Data sets

Additional data sets used to illustrate ordination techniques

glass
Glass composition data
qswur_usa
U.S. university rankings

Tidy ordination

The ‘tbl_ord’ class wrapper, with methods for accessing components and for querying and manipulating metadata

recover_rows() recover_cols() get_rows() get_cols() as.matrix(<tbl_ord>) recover_inertia() recover_coord() get_coord() get_inertia() dim(<tbl_ord>)
Access factors, coordinates, and metadata from ordination objects
recover_aug_rows() recover_aug_cols() recover_aug_coord() augment_ord()
Augment factors and coordinates of 'tbl_ord' objects
tidy(<tbl_ord>) glance(<tbl_ord>) fortify(<tbl_ord>)
Tidiers for 'tbl_ord' objects
annotation
Annotate factors of 'tbl_ord' objects
get_negation() revert_negation() negate_ord() negate_to_first_orthant()
Negation of ordination axes
recover_conference() get_conference() revert_conference() confer_inertia()
Confer inertia to factors of a 'tbl_ord' object
recover_supp_rows() recover_supp_cols()
Supplement 'tbl_ord' objects with new data
as_tbl_ord() make_tbl_ord() is_tbl_ord() is.tbl_ord() valid_tbl_ord() un_tbl_ord()
A unified ordination object class
format(<tbl_ord>) print(<tbl_ord>)
Format a tbl_ord for printing
plot(<tbl_ord>) screeplot(<tbl_ord>) biplot(<tbl_ord>)
Plot and biplot methods for 'tbl_ord' objects
pull_factor() pull_rows() pull_cols() rename_rows() rename_cols() select_rows() select_cols() mutate_rows() mutate_cols() transmute_rows() transmute_cols() cbind_rows() cbind_cols() left_join_rows() left_join_cols()
dplyr verbs for tbl_ord factors
ordinate()
Fit an ordination model to a data object

Layered grammar for biplots

Functions to generate and annotate biplots from ‘tbl_ord’ objects, following the layered grammar of graphics

ggbiplot() ord_aes()
Biplots following the grammar of graphics
coord_scaffold()
Convenience coordinate system for scaffolding axes
stat_rows() stat_cols()
Render plot elements for one matrix of an ordination
stat_projection()
Project rows onto columns or vice-versa
geom_origin() geom_unit_circle()
Marker or unit circle at the origin
geom_interpolation()
Render interpolation of new rows from columns (or vice-versa)
theme_scaffold() theme_biplot()
Scaffolding theme
draw_key_line() draw_key_crosslines() draw_key_crosspoint()
Biplot key drawing functions
ordr-ggproto CoordScaffold GeomInterpolation GeomOrigin GeomUnitCircle StatRows StatCols StatProjection StatRowsDensity2d StatColsDensity2d StatRowsDensity2dFilled StatColsDensity2dFilled StatRowsEllipse StatColsEllipse StatRowsCenter StatColsCenter StatRowsStar StatColsStar StatRowsChull StatColsChull StatRowsPeel StatColsPeel StatRowsCone StatColsCone StatRowsDepth StatColsDepth StatRowsDepthFilled StatColsDepthFilled StatRowsScale StatColsScale StatRowsSpantree StatColsSpantree StatRowsBagplot StatColsBagplot StatRowsRule StatColsRule StatRowsProjection StatColsProjection
ggproto classes created and adapted for ordr
geom_rows_point() geom_cols_point() geom_rows_path() geom_cols_path() geom_rows_polygon() geom_cols_polygon() geom_rows_contour() geom_cols_contour() geom_rows_density_2d() geom_cols_density_2d() geom_rows_density_2d_filled() geom_cols_density_2d_filled() geom_rows_text() geom_cols_text() geom_rows_label() geom_cols_label() geom_rows_text_repel() geom_cols_text_repel() geom_rows_label_repel() geom_cols_label_repel() geom_rows_axis() geom_cols_axis() geom_rows_pointranges() geom_cols_pointranges() geom_rows_lineranges() geom_cols_lineranges() geom_rows_isoline() geom_cols_isoline() geom_rows_text_radiate() geom_cols_text_radiate() geom_rows_vector() geom_cols_vector() geom_rows_bagplot() geom_cols_bagplot() geom_rows_rule() geom_cols_rule() geom_rows_interpolation() geom_cols_interpolation()
Convenience geoms for row and column matrix factors
stat_rows_density_2d() stat_cols_density_2d() stat_rows_density_2d_filled() stat_cols_density_2d_filled() stat_rows_ellipse() stat_cols_ellipse() stat_rows_center() stat_cols_center() stat_rows_star() stat_cols_star() stat_rows_chull() stat_cols_chull() stat_rows_peel() stat_cols_peel() stat_rows_cone() stat_cols_cone() stat_rows_depth() stat_cols_depth() stat_rows_depth_filled() stat_cols_depth_filled() stat_rows_scale() stat_cols_scale() stat_rows_spantree() stat_cols_spantree() stat_rows_bagplot() stat_cols_bagplot() stat_rows_rule() stat_cols_rule() stat_rows_projection() stat_cols_projection()
Convenience stats for row and column matrix factors

Class methods

Recovery and augmentation methods for ordination model classes

as_tbl_ord(<cancor_ord>) recover_rows(<cancor_ord>) recover_cols(<cancor_ord>) recover_inertia(<cancor_ord>) recover_coord(<cancor_ord>) recover_conference(<cancor_ord>) recover_supp_rows(<cancor_ord>) recover_supp_cols(<cancor_ord>) recover_aug_rows(<cancor_ord>) recover_aug_cols(<cancor_ord>) recover_aug_coord(<cancor_ord>)
Functionality for canonical correlations
as_tbl_ord(<cmds_ord>) recover_rows(<cmds_ord>) recover_cols(<cmds_ord>) recover_inertia(<cmds_ord>) recover_coord(<cmds_ord>) recover_conference(<cmds_ord>) recover_aug_rows(<cmds_ord>) recover_aug_cols(<cmds_ord>) recover_aug_coord(<cmds_ord>)
Functionality for classical multidimensional scaling objects
as_tbl_ord(<correspondence>) recover_rows(<correspondence>) recover_cols(<correspondence>) recover_inertia(<correspondence>) recover_conference(<correspondence>) recover_coord(<correspondence>) recover_aug_rows(<correspondence>) recover_aug_cols(<correspondence>) recover_aug_coord(<correspondence>)
Functionality for correspondence analysis ('correspondence') objects
as_tbl_ord(<eigen>) recover_rows(<eigen>) recover_cols(<eigen>) recover_inertia(<eigen>) recover_coord(<eigen>) recover_conference(<eigen>) recover_aug_rows(<eigen_ord>) recover_aug_cols(<eigen_ord>) recover_aug_coord(<eigen>) as_tbl_ord(<eigen_ord>) recover_rows(<eigen_ord>) recover_cols(<eigen_ord>) recover_inertia(<eigen_ord>) recover_coord(<eigen_ord>) recover_conference(<eigen_ord>) recover_aug_coord(<eigen_ord>)
Functionality for eigen-decompositions
as_tbl_ord(<factanal>) recover_rows(<factanal>) recover_cols(<factanal>) recover_inertia(<factanal>) recover_coord(<factanal>) recover_conference(<factanal>) recover_supp_rows(<factanal>) recover_aug_rows(<factanal>) recover_aug_cols(<factanal>) recover_aug_coord(<factanal>)
Functionality for factor analysis ('factanal') objects
as_tbl_ord(<kmeans>) recover_rows(<kmeans>) recover_cols(<kmeans>) recover_coord(<kmeans>) recover_aug_rows(<kmeans>) recover_aug_cols(<kmeans>) recover_aug_coord(<kmeans>)
Functionality for k-means clustering ('kmeans') objects
as_tbl_ord(<lda>) as_tbl_ord(<lda_ord>) recover_rows(<lda>) recover_rows(<lda_ord>) recover_cols(<lda>) recover_cols(<lda_ord>) recover_inertia(<lda>) recover_inertia(<lda_ord>) recover_coord(<lda>) recover_coord(<lda_ord>) recover_conference(<lda>) recover_conference(<lda_ord>) recover_aug_rows(<lda>) recover_aug_rows(<lda_ord>) recover_aug_cols(<lda>) recover_aug_cols(<lda_ord>) recover_aug_coord(<lda>) recover_aug_coord(<lda_ord>) recover_supp_rows(<lda>) recover_supp_rows(<lda_ord>)
Functionality for linear discriminant analysis ('lda') objects
as_tbl_ord(<lm>) recover_rows(<lm>) recover_cols(<lm>) recover_coord(<lm>) recover_aug_rows(<lm>) recover_aug_cols(<lm>) recover_aug_coord(<lm>) recover_aug_rows(<glm>) recover_rows(<mlm>) recover_cols(<mlm>) recover_coord(<mlm>) recover_aug_rows(<mlm>) recover_aug_cols(<mlm>) recover_aug_coord(<mlm>)
Functionality for linear model objects
as_tbl_ord(<lra>) recover_rows(<lra>) recover_cols(<lra>) recover_inertia(<lra>) recover_coord(<lra>) recover_conference(<lra>) recover_aug_rows(<lra>) recover_aug_cols(<lra>) recover_aug_coord(<lra>)
Functionality for log-ratio analysis ('lra') objects
as_tbl_ord(<mca>) recover_rows(<mca>) recover_cols(<mca>) recover_inertia(<mca>) recover_conference(<mca>) recover_coord(<mca>) recover_supp_rows(<mca>) recover_aug_rows(<mca>) recover_aug_cols(<mca>) recover_aug_coord(<mca>)
Functionality for multiple correspondence analysis ('mca') objects
as_tbl_ord(<prcomp>) recover_rows(<prcomp>) recover_cols(<prcomp>) recover_inertia(<prcomp>) recover_coord(<prcomp>) recover_conference(<prcomp>) recover_aug_rows(<prcomp>) recover_aug_cols(<prcomp>) recover_aug_coord(<prcomp>)
Functionality for principal components analysis ('prcomp') objects
as_tbl_ord(<princomp>) recover_rows(<princomp>) recover_cols(<princomp>) recover_inertia(<princomp>) recover_coord(<princomp>) recover_conference(<princomp>) recover_supp_rows(<princomp>) recover_aug_rows(<princomp>) recover_aug_cols(<princomp>) recover_aug_coord(<princomp>)
Functionality for principal components analysis ('princomp') objects
as_tbl_ord(<svd_ord>) recover_rows(<svd_ord>) recover_cols(<svd_ord>) recover_inertia(<svd_ord>) recover_coord(<svd_ord>) recover_conference(<svd_ord>) recover_aug_rows(<svd_ord>) recover_aug_cols(<svd_ord>) recover_aug_coord(<svd_ord>)
Functionality for singular value decompositions